Abstract
Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the “YW” cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.
Highlights
IntroductionBraun 2n = 4x = 36, genomes BBCC) is an important member of the family Brassicaceae and is commercially grown for edible vegetable oil, and as vegetable crop in Ethiopia
The linkage disequilibrium (LD) decay distance varied across 17 chromosome, FIGURE 1 | Analysis of the population structure of 81 B. carinata accessions. (A) Estimated LnP(D) of possible clusters (K) from 1 to 10
Using the phenotypic data of six seed quality traits investigated for the 81 diverse lines in two experiments, we identified the markers accounting for genetic variation in seed quality traits by Genome-wide association analysis (GWAS) and compared with the results revealed by Environmenta Genotype × Environmenta
Summary
Braun 2n = 4x = 36, genomes BBCC) is an important member of the family Brassicaceae and is commercially grown for edible vegetable oil, and as vegetable crop in Ethiopia. This crop is being exploited for biodiesel as a source of a renewable energy (Warwick et al, 2006). It consists of the two homologous genomes, B and C, and may have originated as an allotetraploid species as a result of spontaneous hybridization between diploid species; Brassica nigra (2n = 2x = 14, genome BB) and Brassica oleracea (2n = 2x = 18, genome CC) in Ethiopia (Nagaharu, 1935; Lukens et al, 2004; Warwick, 2011). The genomes of B. rapa, B. oleracea, B. napus, B. nigra, and B. juncea have been sequenced and published (Wang et al, 2011; Chalhoub et al, 2014; Liu et al, 2014; Parkin et al, 2014; Yang et al, 2016), while the genome of B. carinata is sequenced but has not been published (Parkin, per comm.)
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